| Previous changeset 12:10566783d718 (2020-11-03) Next changeset 14:1693b2126f30 (2020-12-23) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty" |
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modified:
spectra_plots.xml test-data/Heatmaps_LM8_file16.pdf test-data/Heatmaps_analyze75.pdf test-data/Heatmaps_imzml.pdf test-data/Heatmaps_processed.pdf test-data/Heatmaps_rdata.pdf test-data/centroids_proc.pdf test-data/preprocessing_results1.ibd test-data/preprocessing_results1.imzml test-data/preprocessing_results1.imzml.txt test-data/preprocessing_results1.pdf test-data/preprocessing_results2.ibd test-data/preprocessing_results2.imzml test-data/preprocessing_results2.imzml.txt test-data/preprocessing_results2.pdf test-data/preprocessing_results3.ibd test-data/preprocessing_results3.imzml test-data/preprocessing_results3.imzml.txt test-data/preprocessing_results3.pdf |
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| diff -r 10566783d718 -r c5aa9fca18c6 spectra_plots.xml --- a/spectra_plots.xml Tue Nov 03 23:11:11 2020 +0000 +++ b/spectra_plots.xml Sun Nov 29 23:41:23 2020 +0000 |
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| b'@@ -1,4 +1,4 @@\n-<tool id="cardinal_spectra_plots" name="MSI plot spectra" version="@VERSION@.1">\n+<tool id="cardinal_spectra_plots" name="MSI plot spectra" version="@VERSION@.2">\n <description>\n mass spectrometry imaging mass spectra plots\n </description>\n@@ -66,23 +66,20 @@\n ## read and extract x,y, optional annotation information\n spectra_tabular = read.delim("$pixel_conditional.pixel_file", header = $pixel_conditional.tabular_pixel_header, stringsAsFactors = FALSE)\n \n- #if $pixel_conditional.column_pixel_annotation:\n+ #if str($pixel_conditional.single_or_overlaid.plot_type) == \'overlaid_plots\':\n \n- spectra_input = spectra_tabular[,c($pixel_conditional.column_pixel_x, $pixel_conditional.column_pixel_y, $pixel_conditional.column_pixel_annotation)]\n+ spectra_input = spectra_tabular[,c($pixel_conditional.column_pixel_x, $pixel_conditional.column_pixel_y, $pixel_conditional.single_or_overlaid.column_pixel_annotation)]\n colnames(spectra_input) = c("x", "y", "annotation")\n+ spectra_input\\$annotation = as.character(spectra_input\\$annotation)\n \n- input_pixels = paste(spectra_input[,1], spectra_input[,2], sep="_")\n- dataset_pixels = paste(coord(msidata)\\$x, coord(msidata)\\$y, sep="_")\n- pixelsofinterest = dataset_pixels %in% input_pixels\n- msidata = msidata[,pixelsofinterest]\n+ msidata_coordinates = data.frame(coord(msidata)\\$x, coord(msidata)\\$y)\n+ colnames(msidata_coordinates) = c("x", "y")\n+ merged_annotation = merge(msidata_coordinates, spectra_input, by=c("x", "y"))\n+ merged_annotation[is.na(merged_annotation)] = "NA"\n \n- ## merge with coordinate information of msidata\n- msidata_coordinates = data.frame(coord(msidata)\\$x, coord(msidata)\\$y, c(1:ncol(msidata)))\n- colnames(msidata_coordinates) = c("x", "y", "pixel_index")\n- merged_annotation = merge(msidata_coordinates, spectra_input, by=c("x", "y"), all.x=TRUE)\n- merged_annotation[is.na(merged_annotation)] = "NA"\n- merged_annotation = merged_annotation[order(merged_annotation\\$pixel_index),]\n- msidata\\$annotation = factor(merged_annotation[,4], levels = unique(as.character(merged_annotation[,4]))) ## keep the right order\n+ merged_annotation = merged_annotation[order(merged_annotation\\$annotation),]\n+ msidata\\$annotation = factor(merged_annotation\\$annotation)\n+\n \n ## overview plot over annotated samples\n number_combined = length(levels(msidata\\$annotation))\n@@ -100,7 +97,21 @@\n legend_size = 6\n }\n \n- position_df = data.frame(coord(msidata)\\$x, coord(msidata)\\$y, as.factor(msidata\\$annotation))\n+ ## colours selection:\n+\n+ #if str($pixel_conditional.single_or_overlaid.colour_conditional.colour_type) == "manual_colour"\n+ #set $color_string = \',\'.join([\'"%s"\' % $color.annotation_color for $color in $pixel_conditional.single_or_overlaid.colour_conditional.colours])\n+ colourvector = c($color_string)\n+\n+ #elif str($pixel_conditional.single_or_overlaid.colour_conditional.colour_type) == "colourpalette"\n+\n+ number_levels = (length(levels(msidata\\$annotation)))\n+\n+ \t colourvector = noquote($pixel_conditional.single_or_overlaid.colour_conditional.palettes)(number_levels)\n+\n+ #end if\n+\n+ position_df = merged_annotation\n colnames(position_df) = c("x", "y", "sample_name")\n \n combine_plot = ggplot(position_df, aes(x=x, y=y, fill=sample_name))+\n@@ -111,15 +122,18 @@\n theme(plot.title = element_text(hjust '..b'ct" label="Separate plot per spectrum or overlaid plot with average spectra per annotation group">\n+\t\t <option value="separate_plots" selected="True" >Separate spectra plots</option>\n+\t\t <option value="overlaid_plots">Overlaid spectra plots</option>\n+\t\t </param>\n+\t\t <when value="separate_plots"/>\n+\t\t <when value="overlaid_plots">\n+\t\t <param name="column_pixel_annotation" data_ref="pixel_file" label="Select column with annotations" type="data_column"/>\n+\t\t <conditional name="colour_conditional">\n+\t\t <param name="colour_type" type="select" label="Choose a colour scheme">\n+\t\t\t <option value="colourpalette" selected="True" >Colour palette</option>\n+\t\t\t <option value="manual_colour">Manual selection</option>\n+\t\t\t</param>\n+\t\t\t<when value="manual_colour">\n+\t\t\t <repeat name="colours" title="Colours for the plots" min="1" max="50">\n+\t\t\t <param name="annotation_color" type="color" label="Colours" value="#ff00ff" help="Numbers of colours should be the same as number of components">\n+\t\t\t <sanitizer>\n+\t\t\t <valid initial="string.letters,string.digits">\n+\t\t\t <add value="#" />\n+\t\t\t </valid>\n+\t\t\t </sanitizer>\n+\t\t\t </param>\n+\t\t\t </repeat>\n+\t\t\t</when>\n+\t\t\t<when value="colourpalette">\n+\t\t\t <param name="palettes" type="select" display="radio" label="Select a colourpalette">\n+\t\t\t <option value="hue_pal()" selected="True">hue</option>\n+\t\t\t <option value="rainbow">rainbow</option>\n+\t\t\t\t<option value="heat.colors">heat colors</option>\n+\t\t\t\t<option value="terrain.colors">terrain colors</option>\n+\t\t\t\t<option value="topo.colors">topo colors</option>\n+\t\t\t\t<option value="cm.colors">cm colors</option>\n+\t\t\t </param>\n+\t\t\t</when>\n+\t\t </conditional>\n+ </when>\n+ </conditional>\n </when>\n <when value="all_pixel">\n </when>\n@@ -554,19 +616,33 @@\n <param name="pixel_file" value="annotations.tabular"/>\n <param name="column_pixel_x" value="1"/>\n <param name="column_pixel_y" value="2"/>\n- <param name="column_pixel_annotation" value="4"/>\n <param name="tabular_pixel_header" value="TRUE"/>\n+\n+ <conditional name="single_or_overlaid">\n+ <param name="plot_type" value="overlaid_plots"/>\n+ <param name="column_pixel_annotation" value="4"/>\n+ <param name="colour_type" value="manual_colour"/>\n+ <repeat name="colours">\n+ <param name="annotation_color" value="#0000FF"/>\n+\t\t </repeat>\n+\t\t <repeat name="colours">\n+\t\t\t<param name="annotation_color" value="#00C957"/>\n+\t\t </repeat>\n+\t\t <repeat name="colours">\n+\t\t\t<param name="annotation_color" value="#B0171F"/>\n+\t\t </repeat>\n+ </conditional>\n </conditional>\n- <param name="fullmz" value="FALSE"/>\n- <conditional name="mz_range">\n- <param name="mz_range_options" value="manual_mz"/>\n- <repeat name="zoomed_sample">\n- <param name="xlimmin" value="1250"/>\n- <param name="xlimmax" value="1270"/>\n- </repeat>\n- </conditional>\n- <param name="grid_variable" value="FALSE"/>\n- <output name="plots" file="Plot_analyze75_allpixels.pdf" compare="sim_size"/>\n+\t\t<param name="fullmz" value="FALSE"/>\n+\t\t<conditional name="mz_range">\n+\t\t <param name="mz_range_options" value="manual_mz"/>\n+\t\t <repeat name="zoomed_sample">\n+\t\t <param name="xlimmin" value="1250"/>\n+\t\t <param name="xlimmax" value="1270"/>\n+\t\t </repeat>\n+\t\t</conditional>\n+\t\t<param name="grid_variable" value="FALSE"/>\n+\t <output name="plots" file="Plot_analyze75_allpixels.pdf" compare="sim_size"/>\n </test>\n <test>\n <param name="infile" value="3_files_combined.RData" ftype="rdata"/>\n' |
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| diff -r 10566783d718 -r c5aa9fca18c6 test-data/preprocessing_results1.imzml --- a/test-data/preprocessing_results1.imzml Tue Nov 03 23:11:11 2020 +0000 +++ b/test-data/preprocessing_results1.imzml Sun Nov 29 23:41:23 2020 +0000 |
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| b'@@ -9,8 +9,8 @@\n \t\t<fileContent>\n \t\t\t<cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value="" />\n \t\t\t<cvParam cvRef="MS" accession="MS:1000127" name="centroid spectrum" value="" />\n-\t\t\t<cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="07177fdd-3760-4df6-8fe2-53d28b280ae8" />\n-\t\t\t<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="749fe32c8243da06001cf4643c5ce4f1ef5a98a8" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="22bd3147-231d-4076-b6bd-67c1fa7c6ef3" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="831eba0fc850529d1351bcbb1baf779fe0773e1b" />\n \t\t\t<cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" />\n \t\t</fileContent>\n \t</fileDescription>\n@@ -86,15 +86,15 @@\n \t\t\t\t\t<binaryDataArray encodedLength="0">\n \t\t\t\t\t\t<referenceableParamGroupRef ref="mzArray" />\n 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| @@ -1,4 +1,4 @@ imzML file: total 24 --rw-rw-r-- 1 meli meli 216 Oct 5 19:57 ibd --rw-rw-r-- 1 meli meli 18090 Oct 5 19:57 imzml +-rw-rw-r-- 1 meli meli 336 Nov 29 01:14 ibd +-rw-rw-r-- 1 meli meli 18092 Nov 29 01:14 imzml |
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| diff -r 10566783d718 -r c5aa9fca18c6 test-data/preprocessing_results2.imzml.txt --- a/test-data/preprocessing_results2.imzml.txt Tue Nov 03 23:11:11 2020 +0000 +++ b/test-data/preprocessing_results2.imzml.txt Sun Nov 29 23:41:23 2020 +0000 |
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| @@ -1,4 +1,4 @@ imzML file: total 64 --rw-rw-r-- 1 meli meli 37404 Oct 5 19:57 ibd --rw-rw-r-- 1 meli meli 22796 Oct 5 19:57 imzml +-rw-rw-r-- 1 meli meli 37404 Nov 29 18:03 ibd +-rw-rw-r-- 1 meli meli 22796 Nov 29 18:03 imzml |
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| diff -r 10566783d718 -r c5aa9fca18c6 test-data/preprocessing_results2.pdf |
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| diff -r 10566783d718 -r c5aa9fca18c6 test-data/preprocessing_results3.ibd |
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| Binary file test-data/preprocessing_results3.ibd has changed |
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| diff -r 10566783d718 -r c5aa9fca18c6 test-data/preprocessing_results3.imzml --- a/test-data/preprocessing_results3.imzml Tue Nov 03 23:11:11 2020 +0000 +++ b/test-data/preprocessing_results3.imzml Sun Nov 29 23:41:23 2020 +0000 |
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| diff -r 10566783d718 -r c5aa9fca18c6 test-data/preprocessing_results3.imzml.txt --- a/test-data/preprocessing_results3.imzml.txt Tue Nov 03 23:11:11 2020 +0000 +++ b/test-data/preprocessing_results3.imzml.txt Sun Nov 29 23:41:23 2020 +0000 |
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| diff -r 10566783d718 -r c5aa9fca18c6 test-data/preprocessing_results3.pdf |
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| Binary file test-data/preprocessing_results3.pdf has changed |